Turgut şekerler

Turgut şekerler
Marmara University · Department of Biochemistry

Doctor of Philosophy

About

15
Publications
4,189
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90
Citations
Introduction
Turgut şekerler currently works at the Department of Biochemistry, Marmara University. Turgut does research in Cancer Research, Biochemistry and Clinical Chemistry. Their most recent publication is 'Protective Effect of Ferulic Acid on Cisplatin Induced Nephrotoxicity in Rats'.
Additional affiliations
March 2014 - November 2015
Marmara University
Position
  • resarch assistant

Publications

Publications (15)
Article
Full-text available
The prothrombotic and inflammatory state plays a significant role in the occurrence of cardiovascular complications in type 2 diabetes mellitus. In this study, the antidiabetic, anti‐inflammatory, and antiplatelet potentials of the extracts obtained from Ribes rubrum were investigated. The antidiabetic, anti‐inflammatory, and antioxidant activities...
Article
Full-text available
We evaluated the effects of Rubus tereticaulis in healing process by determining the total carbonyl content, collagen synthesis, and total protein level on rat wounded tissues. Wounds were performed in the back of 54 Wistar rats, using a biopsy punch instrument with 0.6 mm in diameter. Rats were randomly divided into three groups: (i) un-treatment...
Article
Full-text available
The aim of this study was to investigate in vitro cytotoxic effects of previously isolated compounds (taraxasterol, salvigenin, 3'-O-methyleupatorin, oleanolic acid, jaceosidin and pectolinarigenin) from Centaurea kilaea chloroform extract on hepatocellular carcinoma cell lines, HepG2 and Hep3B, as well as to evaluate the effect on the normal cell...
Article
Full-text available
Violacein is a natural violet pigment produced by various bacterial species, especially by the Gram-negative bacteria Chromobacterium violaceum. Violacein has antibacterial, antifungal, antioxidant and anticancer activities and has various applications in food, cosmetic, textile and pharmaceutical industries. In this study, violacein was extracted...
Article
Full-text available
Resveratrol (RSV) is a natural polyphenolic compound having antioxidant effects. This study was designed to investigate the protective effects of resveratrol against oxidative stress in hepatic ischemia–reperfusion (I/R) injury in streptozotocin (STZ)-induced diabetic rats. STZ was injected intraperitonally (i.p.) to 18 Sprague–Dawley albino rats,...
Article
Full-text available
The effects of aqueous‐ethanol extract of Horse chestnut (HCE) on MMP‐1 and MMP‐9 expressions during cutaneous wound healing in diabetic rats were investigated in this study. The expressions of MMP‐1 and MMP‐9, wound closure, myeloperoxidase (MPO) activity, hydroxyproline, and malondialdehyde (MDA) levels in wound tissue were measured. Quercetin gl...
Article
Full-text available
The aim of this study was to investigate the anticancer activities of five chloroform extracts prepared from the aerial parts of Centeura kilaea Boiss. (CKC), C. cuneifolia Sm. (CCC), C. salicifolia M.Bieb. ex Willd. (CSAC), C. stenolepis Kerner (CSC1 and CSC2) against hepatocellular cancer HepG2 cell line. At the same time, antioxidant and anti-in...
Article
Background Hydrazide-hydrazones constitute an important class of compounds for new drug development. In this study, a series of 39 new acylhydrazones (3-41), derived from (2S)-3-methyl- 2-[[(4-methylphenyl)sulfonyl]amino]butanoic acid hydrazide were synthesized with further aim to achieve biologically active acylhydrazones carrying an amino acid si...
Article
This study aims to determine the potential protective effects of ferulic acid against cisplatin-induced nephrotoxicity and to compare its effect with curcumin, a well-known protective agent against cisplatin- induced toxicity in rats. Administration of cisplatin resulted in high BUN (Blood Urea Nitrogen), creatinine, MDA (Malondialdehyde), MPO (Mye...
Poster
Full-text available
Anticancer Activities of Violacein Extracted From Chromobacterium violaceum ATCC 12472
Poster
Full-text available
Humic acid (HA) is a natural product which is forming during decomposition of organic matter in humus. In recent years, there are some resarches on the medical use of HA. The present study was undertaken in order to evaluate the anticancer properties of the HA using a prostate cancer and osteosarcome cell lines PC-3, SJSA1 as anin vitro model syste...
Article
Context: Cotinus coggygria Scop. (Anacardiaceae) leaves that were used as wound healing in traditional Balkan and Anatolian folk medicine, could be potentially effective in treating diabetic wounds. Objective: This study investigates biochemical and histological effects of ethanol extract of C. coggygria (CCE) on excision wound model in diabetic...
Article
Diabetes is an increasing worldwide health problem. It is well known that diabetes causes brain damage. The mechanism by which diabetes increases brain damage is still elusive. The objective of this study was to determine the effects of streptozotocin-induced diabetes on rat brain tissue. Twenty rats were divided into control and experimental group...

Questions

Questions (9)
Question
Let's say we have an inhibitor with known activity, we chose this ligand as a reference. We then tested other ligands at the same active site and looked for protein-ligand interactions. We saw which amino acids it bonds with. My question is: can it be calculated in % how similar the binding site is to the reference with the ligands tested? I saw this calculation in an article (see:screenshot) and couldn't find how it's done. Does anyone have any ideas on how to do it, using which software?
Question
hi everyone!
I want to validate my docking using chimera software, so I want to redocking . Anyone know the way around this? can i do it like this? = If I select the one with the best score (3.1) and my pure protein from my result file after docking and type rmsd #protein #3.1 on the command line, will it give me the rmsd value?
my second question is about: After getting my result files, I get a score ranking. There, rmsd lb and rmsd ub value are 0, should I take the value given at the beginning? (rmsd lb and ub value 0 one.)
Question
Hello;
I want to do molecular docking with the FTO protein. PDB identity of this protein: 3LFM. While doing the docking process, I will delete the inhibitors named 3-methylthymidine and N-OXALYLGLYCINE, and prepare the pdbqt file, where I will do the hydrogen addition and the charge addition. My question is: Apart from these two chemical residues, there is also an iron atom group in the structure. Should I delete this iron atom as well?
Question
Based on the literature, I screened up to 50 ligands among many ligands to do molecular docking. My question is: can I pre-screen these 50 molecules? with using a software or server. Is there a server where I can score these 50 molecules and estimate their interest in my target protein? Therefore, I could reduce 50 molecules to 5-10 molecules and dock them without wasting time by docking them separately.
Question
For example let's say I have 25 ligands and a single target protein. I would like to screen these ligands based on whether they already have good docking score and then do a detailed docking analysis. For example, I ranked them by dock score and rmsd value and I want to make a detailed analysis of the best 5 remaining ones.
To do this I installed prx software. We used the make ligands command and make the protein macromolecule in the Pyrx software. Next, when I downloaded my protein to the pdb bank, I marked its native ligand and aligned my grid box accordingly. Do I need to delete this marked ligand before docking? Or
Can anyone suggest an alternative way to pre-evaluate the ligands?
Question
There is a graph of the bonds made by the ligand and the protein. Looking at this graph, we see the contribution of bond types. However, gauss1 and gauss 2 bonds I could not understand what type of bond was mentioned. In summary, how to interpret the contribution of gauss 1 and gauss 2 by looking at this graph.Does gauss 1, gauss 2 and repulsion totally give us the effect of vander walls forces?

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